merqury
| Perfect-bacterial-genome-tutorial | merqury | |
|---|---|---|
| 2 | 3 | |
| 109 | 261 | |
| - | 5.0% | |
| 4.5 | 6.4 | |
| 3 months ago | 4 months ago | |
| Python | Shell | |
| - | GNU General Public License v3.0 or later |
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Perfect-bacterial-genome-tutorial
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Bacterial WGS reads and assembly quality questions
I have ONT and Illumina reads for a bacterial WGS (1.8 Mb) and I'm following Ryan Wick's methods for "perfect bacterial genome assembly" (https://github.com/rrwick/Perfect-bacterial-genome-tutorial). I've ran into a few questions I have not been able to find answers to. I'm a grad student struggling in a mostly clinical lab.
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Is Unicycler the best option for hybrid genome assembly?
You should read this https://github.com/rrwick/Perfect-bacterial-genome-tutorial
merqury
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which tool is recommended for kmer based analysis to compare draft genome and sequencing reads.
KAT or merqury. Avoid QUAST.
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Is Unicycler the best option for hybrid genome assembly?
Yeah, Unicycler is solid. iirc Unicycler v5.0+ removes Pilon, so you'll still want to polish your final assembly with your short reads. I like using QV as a quick way to see if I should polish more or not.
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Deciding on genome assembly software
I would recommend using Merqury to see the completeness and quality of your assembly. https://github.com/marbl/merqury
What are some alternatives?
plassembler - Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
quast - Genome assembly evaluation tool
ALE - Assembly Likelihood Estimator
EukCC - Tool to estimate genome quality of microbial eukaryotes
Scoary - Pan-genome wide association studies
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
CompareGenomeQualities - Reference free comparison of genome assemblies
KAT - The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.